[gmx-users] v-rescale fatal error

[Mark Abraham]

Hi Kester,

Glad it's resolved. I am curious what (H3O+?) molecule definition led to
that computation of the DOF? That code is not tested at all...

Mark

On Fri, Oct 10, 2014 at 2:03 PM, Kester Wong <Kester2014 at ibs.re.kr> wrote:

> Hi Justin and all,
>
>
> The same mistake will not be repeated.
>
> The ions are now defined in the residuetypes.dat file and should be
> grouped together.
>
>
>
> -From lessons learned, comes better performance.
>
> Thank you all.
>
> Kester
> --------- 원본 메일 ---------
>
> *보낸사람* : Justin Lemkul <jalemkul at vt.edu>
> *받는사람* : <gmx-users at gromacs.org>
> *받은날짜* : 2014년 10월 10일(금) 20:38:56
> *제목* : Re: [gmx-users] v-rescale fatal error
>
> On 10/10/14 7:36 AM, Kester Wong wrote:
> > Hi Mark,
> >
> >
> > I think it was due to the charged groups in  my temp. coupling setting; I had
> > the H3O cation(s) and Cl anion(s) grouped separately:
> >
> > tc-grps                  = GRA SOL H3O Cl-
> >
> > ; Time constant (ps) and reference temperature (K)
> >
> > tau-t                    = 0.5 0.5 0.5 0.5
> >
> > ref-t                    = 300 300 300 300
> >
> >
> > Calculations run fine once I grouped the ions together, or water+ions.
> >
>
> You shouldn't couple ions separately from the solvent; that's just not stable.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441http://mackerell.umaryland.edu/~jalemkul
>
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